The utility of pathogen genomics: Metagenomics
Description: The utility of pathogen genomics: Metagenomics surveillance for emerging threats 25 September 2025 Metagenomics and its public health applications Developments in diagnostic capabilities: Culturing an organism in the lab on a plate
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slide1. The utility of pathogen genomics: Metagenomics surveillance for emerging threats 25 September 2025<br>
slide2. Metagenomics and its public health applications Developments in diagnostic capabilities:
Culturing an organism in the lab on a plate
Polymerase chain reaction (PCR) which can detect organisms rapidly directly from clinical samples
Whole genome sequencing: sequences the entire genome of a particular pathogen
Metagenomics: can be done direct from clinical samples, and is pathogen agnostic; it sequences everything in a sample Applications of metagenomics in public health<br>
slide3. Metagenomics: mSCAPE: national surveillance pilot platform Metagenomics Surveillance Collaboration and Analysis programme (mSCAPE)
This is a pilot study which will ingest metagenomic data from a number of different sources:
Public domain datasets, research cohorts e.g. SIREN which is a study of healthcare workers
Data from the NHS clinical services
Samples from returning travellers at the Rare and Imported Pathogens laboratory
Newer data sources coming online including environmental pilots using aircraft wastewater
Samples from patients with neurological disease<br>
slide4. Advancing Metagenomic Surveillance in Brazil Brazil highlighted metagenomics as a transformative approach to early detection, outbreak response, and research, with a focus on respiratory viruses during and after the COVID-19 pandemic. Here are some highlights:
Pathogen Dynamics and Metagenomics in Clinical Settings
Understanding spillover events and pathogen dynamics prior to outbreaks is essential for timely intervention.
Metagenomic Surveillance of Respiratory Viruses During the SARS-CoV-2 Pandemic
A longitudinal household-based study was conducted in Salvador, Brazil, to monitor respiratory virus infections during the COVID-19 pandemic.
The ÆSOP Project: Integrating Next-Generation Sequencing (NGS) into Early Warning Systems
The ÆSOP initiative aimed to incorporate NGS-driven pathogen characterization into syndromic surveillance for timely detection of respiratory outbreaks.
Metagenomics provides a pathogen-agnostic diagnostic approach capable of identifying both expected and unexpected infectious agents across clinical and community settings.<br>
slide5. EPI-WIN webinar View webinar “The utility of pathogen genomics: Metagenomics surveillance for emerging threats”
Speakers
Josefina Campos, WHO Berlin Hub
Anna Aryee, UK Health Security Agency (UKHSA)
Ricardo Cunha, Fundação Oswaldo Cruz (FioCruz), Brazil
Erik Karlsson, Institut Pasteur Cambodia
Greg Armstrong, Taskforce for Global Health
Caxton Murira, Science For Africa Foundation<br>
slide2. Metagenomics and its public health applications Developments in diagnostic capabilities:
Culturing an organism in the lab on a plate
Polymerase chain reaction (PCR) which can detect organisms rapidly directly from clinical samples
Whole genome sequencing: sequences the entire genome of a particular pathogen
Metagenomics: can be done direct from clinical samples, and is pathogen agnostic; it sequences everything in a sample Applications of metagenomics in public health<br>
slide3. Metagenomics: mSCAPE: national surveillance pilot platform Metagenomics Surveillance Collaboration and Analysis programme (mSCAPE)
This is a pilot study which will ingest metagenomic data from a number of different sources:
Public domain datasets, research cohorts e.g. SIREN which is a study of healthcare workers
Data from the NHS clinical services
Samples from returning travellers at the Rare and Imported Pathogens laboratory
Newer data sources coming online including environmental pilots using aircraft wastewater
Samples from patients with neurological disease<br>
slide4. Advancing Metagenomic Surveillance in Brazil Brazil highlighted metagenomics as a transformative approach to early detection, outbreak response, and research, with a focus on respiratory viruses during and after the COVID-19 pandemic. Here are some highlights:
Pathogen Dynamics and Metagenomics in Clinical Settings
Understanding spillover events and pathogen dynamics prior to outbreaks is essential for timely intervention.
Metagenomic Surveillance of Respiratory Viruses During the SARS-CoV-2 Pandemic
A longitudinal household-based study was conducted in Salvador, Brazil, to monitor respiratory virus infections during the COVID-19 pandemic.
The ÆSOP Project: Integrating Next-Generation Sequencing (NGS) into Early Warning Systems
The ÆSOP initiative aimed to incorporate NGS-driven pathogen characterization into syndromic surveillance for timely detection of respiratory outbreaks.
Metagenomics provides a pathogen-agnostic diagnostic approach capable of identifying both expected and unexpected infectious agents across clinical and community settings.<br>
slide5. EPI-WIN webinar View webinar “The utility of pathogen genomics: Metagenomics surveillance for emerging threats”
Speakers
Josefina Campos, WHO Berlin Hub
Anna Aryee, UK Health Security Agency (UKHSA)
Ricardo Cunha, Fundação Oswaldo Cruz (FioCruz), Brazil
Erik Karlsson, Institut Pasteur Cambodia
Greg Armstrong, Taskforce for Global Health
Caxton Murira, Science For Africa Foundation<br>